Wednesday, August 30, 2017

The human genome is pervasively transcribed. More than 80% of the genome is complementary to transcripts that have been detected in some tissue or cell type. The important question is whether most of these transcripts have a biological function. How many genes are there that produce functional non-coding RNA?

There's a reason why this question is important. It's because we have every reason to believe that spurious transcription is common in large genomes like ours. Spurious, or accidental, transcription occurs when the transcription initiation complex binds nonspecifically to sites in the genome that are not real promoters. Spurious transcription also occurs when the initiation complex (RNA plymerase plus factors) fires in the wrong direction from real promoters. Binding and inappropriate transcription are aided by the binding of transcription factors to nonpromoter regions of the genome—a well-known feature of all DNA binding proteins [see Are most transcription factor binding sites functional?].

The meeting was a huge disappointment [Kevin Laland's new view of evolution]. It was dominated by talks that were so abstract and obtuse that it was difficult to mount any serious discussion. The one thing that was crystal clear is that almost all of the speakers had an old-fashioned view of the current status of evolutionary theory. Thus, they were for the most part arguing against a strawman version of evolutionary theory.

Most of these papers are locked behind a paywall and that's a good thing because you won't be tempted to read them. The overall quality is atrocious—the Royal Society should be embarrassed to publish them.1 The only good thing about the meeting was that I got to meet a few friends and acquaintances who were supporters of evolution. There was also a sizable contingent of Intelligent Design Creationists at the meeting and I enjoyed talking to them as well2 [see Intelligent Design Creationists reveal their top story of 2016].

Friday, August 25, 2017

Lots of people misunderstand punctuated equilibria. It's a theory about small changes leading to speciation. In many cases the changes are so slight that you and I might not notice the difference. These are not leaps or saltations and there are no intermediates or missing links. The changes may be due to changes in the frequency of one or two alleles.

Punctuated equilibria are when these speciation events take place relatively quickly and are followed by much longer periods of stasis (no change). Niles Eldredge explains how the theory is derived from his studies of thousands of trilobite fossils.

One of the common rationalizations is to speculate that while humans may have "only" 25,000 genes they are regulated and controlled in a much more sophisticated manner than the genes in other species. It's this extra level of control that makes humans special. Such speculations have been around for almost fifty years but they have gained in popularity since publication of the human genome sequence.

In some cases, the extra level of regulation is thought to be due to abundant regulatory RNAs. This means there must be tens of thousand of extra genes expressing these regulatory RNAs. John Mattick is the most vocal proponent of this idea and he won an award from the Human Genome Organization for "proving" that his speculation is correct! [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research]. Knowledgeable scientists know that Mattick is probably wrong. They believe that most of those transcripts are junk RNAs produced by accidental transcription at very low levels from non-conserved sequences.

Monday, August 07, 2017

Paul Draper is a philosopher at Purdue University (West Lafayette, Indiana, USA). He has just (Aug. 2, 2017) posted an article on Atheism and Agnosticism on the Stanford Encyclopedia of Philosophy website.

Many philosphers use a different definition of atheism than many atheists. Philosophers tend to define atheism as the proposition that god(s) do not exist. Many atheists (I am one) define atheism as the lack of belief in god(s). The distinction is important but for now I want to discuss Draper's defense of agnosticism.

Keep in mind that Draper defines atheism as "god(s) don't exist." He argues, convincingly, that this proposition cannot be proven. He also argues that theism—the proposition that god(s) exist—can also not be proven. Therefore, the only defensible position for a philosopher like him is agnosticism.

Friday, August 04, 2017

Now that I'm officially retired I've been cleaning out my office at the university and transferring all the important stuff to my home office. I'm taking advantage of this opportunity to throw out everything that I don't want any more. Eventually I'll have to vacate my university office because it's due to be renovated and transferred to another department.

Some stuff is easy to toss out and some stuff is easy to keep. It's the other stuff that causes a problem. Here's an example ....

These are the manuals that came with my very first PC back in 1981. I know I'll never use them but I'm kinda attached to them. Are they antiques yet?

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.